I have Matlab installed on my computer and there is always an .exe running in the background called matlabserver.exe. Looking through the help files, it seems to allow Matlab to see internet, use ...

This is a valid program, but it is up to you whether or not you want it to run on startup. Whether or not you need to run this program on startup must be decided by you. If you feel that you want this ...

isn't ! used in Matlab to run command line stuff? I don't know if you could use it to feed additional parameters to a running program, but its a start, I suppose.